[2024-01-24 13:55:19,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d2901c9-fa57-49a6-b65c-bf6c69cdb416/dqc_reference
[2024-01-24 13:55:21,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,144] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ce48e64-83f1-4820-b9ad-345411f0b92a/GCF_000313565.1_ASM31356v2_genomic.fna.gz | prodigal -d GCF_000313565.1_ASM31356v2_genomic.fna/cds.fna -a GCF_000313565.1_ASM31356v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:29,318] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:29,319] [INFO] Task started: HMMsearch
[2024-01-24 13:55:29,319] [INFO] Running command: hmmsearch --tblout GCF_000313565.1_ASM31356v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d2901c9-fa57-49a6-b65c-bf6c69cdb416/dqc_reference/reference_markers.hmm GCF_000313565.1_ASM31356v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:29,756] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:29,757] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ce48e64-83f1-4820-b9ad-345411f0b92a/GCF_000313565.1_ASM31356v2_genomic.fna.gz]
[2024-01-24 13:55:29,809] [INFO] Query marker FASTA was written to GCF_000313565.1_ASM31356v2_genomic.fna/markers.fasta
[2024-01-24 13:55:29,809] [INFO] Task started: Blastn
[2024-01-24 13:55:29,809] [INFO] Running command: blastn -query GCF_000313565.1_ASM31356v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2901c9-fa57-49a6-b65c-bf6c69cdb416/dqc_reference/reference_markers.fasta -out GCF_000313565.1_ASM31356v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:30,458] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:30,461] [INFO] Selected 24 target genomes.
[2024-01-24 13:55:30,461] [INFO] Target genome list was writen to GCF_000313565.1_ASM31356v2_genomic.fna/target_genomes.txt
[2024-01-24 13:55:30,476] [INFO] Task started: fastANI
[2024-01-24 13:55:30,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce48e64-83f1-4820-b9ad-345411f0b92a/GCF_000313565.1_ASM31356v2_genomic.fna.gz --refList GCF_000313565.1_ASM31356v2_genomic.fna/target_genomes.txt --output GCF_000313565.1_ASM31356v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:42,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:42,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d2901c9-fa57-49a6-b65c-bf6c69cdb416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:42,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d2901c9-fa57-49a6-b65c-bf6c69cdb416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:42,109] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:42,110] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:42,110] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Dielma fastidiosa	strain=JC13	GCA_000313565.2	1034346	1034346	type	True	99.9998	1178	1179	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:55:42,111] [INFO] DFAST Taxonomy check result was written to GCF_000313565.1_ASM31356v2_genomic.fna/tc_result.tsv
[2024-01-24 13:55:42,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:42,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:42,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d2901c9-fa57-49a6-b65c-bf6c69cdb416/dqc_reference/checkm_data
[2024-01-24 13:55:42,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:42,158] [INFO] Task started: CheckM
[2024-01-24 13:55:42,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000313565.1_ASM31356v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000313565.1_ASM31356v2_genomic.fna/checkm_input GCF_000313565.1_ASM31356v2_genomic.fna/checkm_result
[2024-01-24 13:56:13,460] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:13,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:13,480] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:13,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:13,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000313565.1_ASM31356v2_genomic.fna/markers.fasta)
[2024-01-24 13:56:13,482] [INFO] Task started: Blastn
[2024-01-24 13:56:13,482] [INFO] Running command: blastn -query GCF_000313565.1_ASM31356v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2901c9-fa57-49a6-b65c-bf6c69cdb416/dqc_reference/reference_markers_gtdb.fasta -out GCF_000313565.1_ASM31356v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:14,364] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:14,368] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:14,368] [INFO] Target genome list was writen to GCF_000313565.1_ASM31356v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:14,391] [INFO] Task started: fastANI
[2024-01-24 13:56:14,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce48e64-83f1-4820-b9ad-345411f0b92a/GCF_000313565.1_ASM31356v2_genomic.fna.gz --refList GCF_000313565.1_ASM31356v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000313565.1_ASM31356v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:22,518] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:22,529] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:22,529] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000313565.1	s__Dielma fastidiosa	99.9998	1178	1179	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Dielma	95.0	98.62	98.01	0.93	0.87	8	conclusive
GCA_001305055.1	s__Dielma sp001305055	92.63	921	1179	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Dielma	95.0	98.81	98.81	0.91	0.91	3	-
GCF_014337235.1	s__NSJ-61 sp003433845	80.3903	85	1179	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__NSJ-61	95.0	99.54	98.10	0.85	0.77	12	-
GCF_900104665.1	s__Traorella massiliensis	77.3958	66	1179	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Traorella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:22,531] [INFO] GTDB search result was written to GCF_000313565.1_ASM31356v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:22,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:22,535] [INFO] DFAST_QC result json was written to GCF_000313565.1_ASM31356v2_genomic.fna/dqc_result.json
[2024-01-24 13:56:22,535] [INFO] DFAST_QC completed!
[2024-01-24 13:56:22,536] [INFO] Total running time: 0h1m3s